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Table 1 (A, B) – Heliconius repetitive elements.

From: Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies

A.

Locus name (origin)

MARINER_HC

(Hyalophora cecropia)

MARI_BM

(Bombyx mori)

GYPSY70-I_AG

(Anopheles gambiae)

Sake_BM

(Bombyx mori)

DOC5_DM

(D. melanogaster)

G4_DM

(D. melanogaster)

ZENON_BM

(Bombyx mori)

    

Element Family

Mariner

Mariner

Gypsy

Daphne

Jockey

Jockey

CR1

    

Element type

DNA transposon

DNA transposon

LTR retroposon

LTR retroposon

Non-LTR retroposon

Non-LTR retroposon

Non-LTR retroposon

    

Described length

1255

1310

4858

5140

2791

3856

2599

    
 

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

    

# regions masked

3

NA

3

NA

NA

1

2

1

5

NA

1

NA

5

1

    

Avg length of masked region (+/- Std.Dev.)

85.33 (51.03)

NA

159.33 (28.11)

NA

NA

2062

253 (173.95)

73

440 (275.77)

NA

1243

NA

520.8 (618.74)

44

    

Min length of masked region

46

NA

127

NA

NA

NA

46

NA

245

NA

NA

NA

94

NA

    

Max length of masked region

143

NA

178

NA

NA

NA

143

NA

635

NA

NA

NA

1574

NA

    

Total nucleotide masked

256

NA

478

NA

NA

2062

256

73

880

NA

1243

NA

2604

44

    

Proportion of BACs masked

0.07%

NA

0.14%

NA

NA

1.05%

0.07%

0.04%

0.25%

NA

0.35%

NA

0.74%

0.02%

    

B.

Core Motif

1

2

3

4

5

6

7

8

8

 

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

era

mel

Length of core motif

469

NA

460

598

428

NA

384

NA

314

NA

259

NA

266

NA*

147

NA

NA

306

# regions masked

16

2

7

11

29

1

5

NA

11

NA

17

4

310

129

40

9

NA

10

Mean length of masked region (Std.Dev.)

225. (121.71)

70.5 (16.26)

415 (118.3)

406.27 (302.12)

166.69 (127.26)

119 (NA)

341.8 (100.7)

NA

189.36 (90.64)

NA

125.59 (92.66)

76.75 (38.87)

155.25 (70.85)

129.95 (64.26)

89.1 (27.99)

80.11 (21.98)

NA

244.1 (96.74)

Minimum length of masked region

69

59

147

29

37

NA

162

NA

38

NA

28

55

38

40

38

55

NA

46

Maximum length of masked region

439

82

470

740

449

NA

394

NA

314

NA

272

135

287

280

148

116

NA

314

Total nucleotide masked

3603

141

2905

4469

4834

119

1709

NA

2083

NA

2135

307

48126

16763

3564

721

NA

2441

Amount of BACs masked

1.0%

0.1%

0.8%

2.3%

1.4%

0.1%

0.5%

NA

0.6%

NA

0.6%

0.2%

13.6%

8.5%

1.0%

0.4%

NA

1.2%

  1. Summary of identification and repeat masking of repetitive elements in BAC sequences from H. erato (accession numbers: AC193804, AC216670) and H. melpomene (accession numbers: CR974474, CT955980). A) Repetitive elements identified via similarity to previously described sequences. B) Novel repetitive elements unique to Heliconius identified de novo using the RepeatMasker software (additional file 1: Novel repetitive elements in Heliconius (row sequences)). Each core motif is a summary sequence representing a different and unique set of related repeat sequences. Motifs four and five were not observed in H. melpomene; Motif nine was not oberseved in H. erato. Core Motifs 1,2,3,4,5,6,7 and 8 were identified by RepeatFinder only in H. erato but masked by RepeatMasker in H. melpomene. (* RepeatFinder identified fragments of this motif in H. melpomene, but the groups did not overlap to give a core motif comparable to that in H. erato).